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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ), 'gf_id' => 'HOM05D001160', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001160' ), 'data_identifier' => 'HOM05D001160', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001160', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '532', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p17950' => 'bna', 'A02p07900' => 'bna', 'A02p08020' => 'bna', 'A02p13820' => 'bna', 'A02p13840' => 'bna', 'A02p13860' => 'bna', 'A02p31500' => 'bna', 'A03p12420' => 'bna', 'A03p14050' => 'bna', 'A03p41780' => 'bna', 'A03p56850' => 'bna', 'A03p57050' => 'bna', 'A05p28330' => 'bna', 'A09p27540' => 'bna', 'A09p27570' => 'bna', 'A09p27980' => 'bna', 'A10p12620' => 'bna', 'A10p16120' => 'bna', 'Aa31LG3G11420' => 'aar', 'Aa31LG3G13880' => 'aar', 'Aa31LG5G12230' => 'aar', 'Aa31LG8G7330' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_369.554' => 'aag', 'Actinidia05044' => 'ach', 'Actinidia06593' => 'ach', 'Actinidia10761' => 'ach', 'Actinidia10762' => 'ach', 'Actinidia20049' => 'ach', 'Actinidia38341' => 'ach', 'Ah.04g166360' => 'amhyb', 'Ah.04g166370' => 'amhyb', 'Ah.14g078470' => 'amhyb', 'AL126U10010' => 'aly', 'AL2G25270' => 'aly', 'AL2G25280' => 'aly', 'AL3G34340' => 'aly', 'AL7G26150' => 'aly', 'AL8G31010' => 'aly', 'AL8G34150' => 'aly', 'AL8G34270' => 'aly', 'Aqoxy1G04053' => 'aox', 'Aqoxy7G03468' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0FVV8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KQYW0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MS0187' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT6VHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TREG0V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TWT7AM' => 'arhy', 'AT1G66970' => 'ath', 'AT1G66980' => 'ath', 'AT3G20520' => 'ath', 'AT4G26690' => 'ath', 'AT5G55480' => 'ath', 'AT5G58050' => 'ath', 'AT5G58170' => 'ath', 'ATR0565G003' => 'atr', 'ATR0712G068' => 'atr', 'Atru.chr12.1605' => 'acertr', 'Atru.chr7.147' => 'acertr', 'AUR62011273' => 'cqu', 'AUR62015925' => 'cqu', 'AUR62029751' => 'cqu', 'AUR62040683' => 'cqu', 'AUR62040684' => 'cqu', 'AUR62042028' => 'cqu', 'BcaB01g01616' => 'bca', 'BcaB01g01660' => 'bca', 'BcaB01g01662' => 'bca', 'BcaB01g02821' => 'bca', 'BcaB01g03717' => 'bca', 'BcaB01g04340' => 'bca', 'BcaB01g04474' => 'bca', 'BcaB05g22398' => 'bca', 'BcaB05g22406' => 'bca', 'BcaB05g24220' => 'bca', 'BcaB05g24224' => 'bca', 'BcaB08g35904' => 'bca', 'BcaB08g36154' => 'bca', 'BcaC01g03552' => 'bca', 'BcaC01g05558' => 'bca', 'BcaC01g06366' => 'bca', 'BcaC03g14127' => 'bca', 'BcaC03g14779' => 'bca', 'BcaC03g14784' => 'bca', 'BcaC03g16990' => 'bca', 'BcaC04g19911' => 'bca', 'BcaC04g21114' => 'bca', 'BcaC04g21160' => 'bca', 'BcaC06g32733' => 'bca', 'BcaC09g50624' => 'bca', 'BcaC09g51382' => 'bca', 'BcaC09g52255' => 'bca', 'BcaNung05848' => 'bca', 'BolC1t02206H' => 'bol', 'BolC2t07466H' => 'bol', 'BolC2t07479H' => 'bol', 'BolC2t08373H' => 'bol', 'BolC2t08374H' => 'bol', 'BolC2t08382H' => 'bol', 'BolC2t10978H' => 'bol', 'BolC3t13902H' => 'bol', 'BolC3t14068H' => 'bol', 'BolC3t14886H' => 'bol', 'BolC3t17405H' => 'bol', 'BolC5t33097H' => 'bol', 'BolC6t38980H' => 'bol', 'BolC7t45990H' => 'bol', 'BolC7t46010H' => 'bol', 'BolC9t56331H' => 'bol', 'BolC9t56384H' => 'bol', 'BolC9t57850H' => 'bol', 'BraA01t01750Z' => 'bra', 'BraA02t05863Z' => 'bra', 'BraA02t05874Z' => 'bra', 'BraA02t06443Z' => 'bra', 'BraA02t06446Z' => 'bra', 'BraA02t08153Z' => 'bra', 'BraA02t08159Z' => 'bra', 'BraA03t10556Z' => 'bra', 'BraA03t10705Z' => 'bra', 'BraA03t13331Z' => 'bra', 'BraA03t14753Z' => 'bra', 'BraA03t14774Z' => 'bra', 'BraA05t21716Z' => 'bra', 'BraA07t30893Z' => 'bra', 'BraA09t38321Z' => 'bra', 'BraA09t38323Z' => 'bra', 'BraA09t38367Z' => 'bra', 'BraA10t43360Z' => 'bra', 'BraA10t43617Z' => 'bra', 'C01p22770' => 'bna', 'C02p13540' => 'bna', 'C02p13670' => 'bna', 'C02p22250' => 'bna', 'C02p22260' => 'bna', 'C02p22310' => 'bna', 'C03p14620' => 'bna', 'C03p16490' => 'bna', 'C03p24940' => 'bna', 'C03p51160' => 'bna', 'C05p43820' => 'bna', 'C06p38870' => 'bna', 'C07p55020' => 'bna', 'C07p55230' => 'bna', 'C09p34850' => 'bna', 'C09p35470' => 'bna', 'C09p46120' => 'bna', 'C09p49970' => 'bna', 'CAN.G23.6' => 'can', 'CAN.G337.43' => 'can', 'CAN.G654.1' => 'can', 'CANSAT11G1138' => 'cansat', 'CANSAT11G2511' => 'cansat', 'CANSAT64G2961' => 'cansat', 'CANSAT78G1449' => 'cansat', 'CARHR059280' => 'chi', 'CARHR059290' => 'chi', 'CARHR059300' => 'chi', 'CARHR059310' => 'chi', 'CARHR059370' => 'chi', 'CARHR059380' => 'chi', 'CARHR096280' => 'chi', 'CARHR188050' => 'chi', 'CARHR234300' => 'chi', 'CARHR263430' => 'chi', 'CARHR263440' => 'chi', 'CARHR268790' => 'chi', 'CARHR271860' => 'chi', 'CARHR271980' => 'chi', 'Carub.0002s1325' => 'cru', 'Carub.0002s1327' => 'cru', 'Carub.0003s2048' => 'cru', 'Carub.0007s1416' => 'cru', 'Carub.0008s1582' => 'cru', 'Carub.0008s1860' => 'cru', 'Carub.0008s1872' => 'cru', 'Carub.0120s0002' => 'cru', 'Ca_06358_v3' => 'car', 'Ca_06359_v3' => 'car', 'Ca_14778_v3' => 'car', 'Ca_21109_v3' => 'car', 'Cc05_g14510' => 'ccan', 'Cc06_g15280' => 'ccan', 'CDE05G1466' => 'cde', 'CDE06G0277' => 'cde', 'CDE06G1422' => 'cde', 'CDE07G0071' => 'cde', 'CDE07G0446' => 'cde', 'Cfa020248' => 'cfa', 'Cfa020850' => 'cfa', 'Ciclev10007536m.g' => 'ccl', 'CiPaw.11G197600' => 'cil', 'CiPaw.11G197800' => 'cil', 'CiPaw.11G198400' => 'cil', 'CiPaw.11G198500' => 'cil', 'CiPaw.11G198800' => 'cil', 'CiPaw.11G198900' => 'cil', 'CiPaw.11G199000' => 'cil', 'CiPaw.11G199100' => 'cil', 'CiPaw.15G173900' => 'cil', 'CiPaw.16G115100' => 'cil', 'ClCG01G019310' => 'cla', 'ClCG09G020970' => 'cla', 'COL.COLO4_09755' => 'col', 'COL.COLO4_18773' => 'col', 'COL.COLO4_20288' => 'col', 'Cpa.g.sc12.217' => 'cpa', 'Cpa.g.sc12.218' => 'cpa', 'Cpa.g.sc12.219' => 'cpa', 'Cpa.g.sc46.122' => 'cpa', 'Cpa.g.sc46.123' => 'cpa', 'CsaV3_6G046000' => 'csa', 'CsaV3_7G018770' => 'csa', 'CSS0006983' => 'camsi', 'CSS0007428' => 'camsi', 'CSS0018550' => 'camsi', 'CSS0027871' => 'camsi', 'CSS0035290' => 'camsi', 'CSS0044496' => 'camsi', 'CSS0049754' => 'camsi', 'DCAR_005316' => 'dca', 'DCAR_009782' => 'dca', 'DCAR_013206' => 'dca', 'DCAR_015381' => 'dca', 'DCAR_016634' => 'dca', 'DCAR_019374' => 'dca', 'DCAR_022600' => 'dca', 'Dinv10295' => 'din', 'Dinv22214' => 'din', 'Dinv22217' => 'din', 'Dinv30336' => 'din', 'Dinv40821' => 'din', 'Dinv41401' => 'din', 'Dinv42886' => 'din', 'Dinv43214' => 'din', 'Duzib150G1511' => 'dzi', 'Duzib168G2054' => 'dzi', 'Duzib170G0733' => 'dzi', 'Duzib187G1790' => 'dzi', 'Duzib213G0157' => 'dzi', 'Duzib268G0029' => 'dzi', 'Duzib268G0229' => 'dzi', 'Duzib268G1560' => 'dzi', 'Duzib268G1598' => 'dzi', 'ECA234G1841' => 'eca', 'ECA236G2990' => 'eca', 'ECA240G0314' => 'eca', 'ECA246G0401' => 'eca', 'ECA246G1928' => 'eca', 'EL10Ac4g07638' => 'bvu', 'EL10Ac8g18841' => 'bvu', 'Eucgr.C00368' => 'egr', 'Eucgr.F03515' => 'egr', 'FAN11G0560' => 'fan', 'FAN11G1921' => 'fan', 'FAN16G0917' => 'fan', 'FAN16G3522' => 'fan', 'FAN17G1129' => 'fan', 'FAN19G0877' => 'fan', 'FAN21G3411' => 'fan', 'FAN23G3064' => 'fan', 'FAN25G1612' => 'fan', 'FAN26G2014' => 'fan', 'FAN28G1955' => 'fan', 'FvH4_1g01240' => 'fve', 'FvH4_3g13670' => 'fve', 'FvH4_3g30290' => 'fve', 'Glyma.02G296400' => 'gma', 'Glyma.08G324300' => 'gma', 'Glyma.08G324401' => 'gma', 'Glyma.08G324500' => 'gma', 'Glyma.08G324600' => 'gma', 'Glyma.13G155100' => 'gma', 'Glyma.14G017100' => 'gma', 'Glyma.17G075750' => 'gma', 'Glyma.18G064851' => 'gma', 'Glyma.18G085400' => 'gma', 'Glyma.18G085451' => 'gma', 'Glyma.18G085500' => 'gma', 'Gohir.A01G085700' => 'ghi', 'Gohir.A04G010400' => 'ghi', 'Gohir.A05G051400' => 'ghi', 'Gohir.D01G072000' => 'ghi', 'Gohir.D05G052900' => 'ghi', 'Gohir.D05G377600' => 'ghi', 'Gorai.002G094900' => 'gra', 'Gorai.009G054700' => 'gra', 'Gorai.009G445400' => 'gra', 'GSVIVG01003731001' => 'vvi', 'GSVIVG01037754001' => 'vvi', 'HanXRQChr05g0159841' => 'han', 'HanXRQChr05g0159981' => 'han', 'HanXRQChr05g0159991' => 'han', 'HanXRQChr08g0233141' => 'han', 'HanXRQChr10g0314621' => 'han', 'HanXRQChr17g0546201' => 'han', 'HanXRQChr17g0546211' => 'han', 'HanXRQChr17g0546221' => 'han', 'HanXRQChr17g0546231' => 'han', 'Haze_09768' => 'cav', 'Haze_19238' => 'cav', 'Hma1.2p1_0028F.1_g017360' => 'hma', 'Hma1.2p1_0134F.1_g061530' => 'hma', 'Hma1.2p1_1199F.1_g266380' => 'hma', 'HPP92_002848' => 'vpl', 'HPP92_004769' => 'vpl', 'HPP92_011619' => 'vpl', 'HPP92_017843' => 'vpl', 'Hund01932' => 'sun', 'Hund21621' => 'sun', 'Hund21622' => 'sun', 'Hund23168' => 'sun', 'Lalb_Chr00c48g0412811' => 'lal', 'Lalb_Chr00c48g0412821' => 'lal', 'Lalb_Chr00c48g0412831' => 'lal', 'Lalb_Chr00c48g0412841' => 'lal', 'Lalb_Chr00c48g0413071' => 'lal', 'Lalb_Chr04g0248061' => 'lal', 'Lalb_Chr04g0248071' => 'lal', 'Lalb_Chr07g0179711' => 'lal', 'Lalb_Chr07g0179731' => 'lal', 'Lalb_Chr10g0107241' => 'lal', 'Lalb_Chr11g0072741' => 'lal', 'Lalb_Chr12g0198581' => 'lal', 'Lalb_Chr13g0300981' => 'lal', 'Lj1C883T2' => 'lonja', 'Lj4g0014158' => 'lja', 'Lj6g0023201' => 'lja', 'Lj6g0027961' => 'lja', 'Lj7C454T4' => 'lonja', 'Lj8A175T72' => 'lonja', 'LjContig00272g0001847' => 'lja', 'Lsat_1_v5_gn_0_15481' => 'lsa', 'Lsat_1_v5_gn_2_85341' => 'lsa', 'Lsat_1_v5_gn_4_122700' => 'lsa', 'Lsat_1_v5_gn_5_3340' => 'lsa', 'Lsat_1_v5_gn_5_91421' => 'lsa', 'Lsat_1_v5_gn_6_10360' => 'lsa', 'Lsat_1_v5_gn_7_113720' => 'lsa', 'Manes.03G134600' => 'mes', 'Manes.14G142100' => 'mes', 'Manes.15G064700' => 'mes', 'Mapoly0155s0023' => 'mpo', 'MBI16_g05833_MAGBIO' => 'mbi', 'MBI16_g31705_MAGBIO' => 'mbi', 'MBI19_g06150_MAGBIO' => 'mbi', 'MD02G1010300' => 'mdo', 'MD03G1190400' => 'mdo', 'MD11G1207100' => 'mdo', 'MD15G1155300' => 'mdo', 'Medtr2g450160' => 'mtr', 'Medtr3g055610' => 'mtr', 'Medtr4g131380' => 'mtr', 'Medtr5g094230' => 'mtr', 'Medtr7g050345' => 'mtr', 'MELO3C007806.2' => 'cme', 'MELO3C013101.2' => 'cme', 'Migut.H01242' => 'egut', 'Migut.H01780' => 'egut', 'Migut.J01322' => 'egut', 'Migut.M01693' => 'egut', 'MSTRG.13006' => 'ama', 'MSTRG.14466' => 'ama', 'MSTRG.15780' => 'ama', 'MSTRG.6110' => 'ama', 'Nitab4.5_0001160g0130' => 'nta', 'Nitab4.5_0002051g0020' => 'nta', 'Nitab4.5_0003869g0060' => 'nta', 'Nitab4.5_0004362g0020' => 'nta', 'Nitab4.5_0005188g0040' => 'nta', 'Nitab4.5_0007899g0030' => 'nta', 'Nn1g00007' => 'nnu', 'Nn1g03299' => 'nnu', 'Nn1g05004' => 'nnu', 'Nn1g07403' => 'nnu', 'Nn1g07406' => 'nnu', 'Nn1g07408' => 'nnu', 'Nn1g07410' => 'nnu', 'Nn5g27559' => 'nnu', 'Oeu005501.1' => 'oeu', 'Oeu005977.1' => 'oeu', 'Oeu029055.1' => 'oeu', 'Oeu052184.1' => 'oeu', 'Oeu052695.1' => 'oeu', 'Os02g0187400' => 'osa', 'Os02g0588500' => 'osa', 'Os04g0472300' => 'osa', 'Os08g0503200' => 'osa', 'Os09g0339800' => 'osa', 'Os12g0456700' => 'osa', 'Peaxi162Scf00285g00945' => 'pax', 'Peaxi162Scf00914g00530' => 'pax', 'Peaxi162Scf01165g00215' => 'pax', 'PGR031G1108' => 'pgr', 'PGR142G0373' => 'pgr', 'PGSC0003DMG400003271' => 'stu', 'PGSC0003DMG400003273' => 'stu', 'PGSC0003DMG400012843' => 'stu', 'PGSC0003DMG400012853' => 'stu', 'PGSC0003DMG400012855' => 'stu', 'PGSC0003DMG400022294' => 'stu', 'PGSC0003DMG400025200' => 'stu', 'Phvul.003G158000' => 'pvu', 'Phvul.006G050300' => 'pvu', 'Phvul.006G050400' => 'pvu', 'Phvul.006G050600' => 'pvu', 'Phvul.006G050800' => 'pvu', 'Phvul.008G274200' => 'pvu', 'Phvul.008G274300' => 'pvu', 'Potri.001G360700' => 'ptr', 'Potri.001G360800' => 'ptr', 'Potri.006G187600' => 'ptr', 'Potri.018G110600' => 'ptr', 'Pp3c1_13780' => 'ppa', 'Pp3c2_26540' => 'ppa', 'Pp3c2_28200' => 'ppa', 'Prupe.4G228400' => 'ppe', 'Prupe.7G259800' => 'ppe', 'Psat1g022200' => 'psa', 'Psat2g010640' => 'psa', 'Psat4g008920' => 'psa', 'Psat5g172160' => 'psa', 'PSO210G3034' => 'pso', 'PSO210G4282' => 'pso', 'PSO210G7237' => 'pso', 'PSO302G0124' => 'pso', 'PSO302G0136' => 'pso', 'PSO302G0229' => 'pso', 'PSO339G5449' => 'pso', 'PSO384G4409' => 'pso', 'PSO384G5065' => 'pso', 'QL02p092537' => 'qlo', 'QL08p008432' => 'qlo', 'RcHm_v2.0_Chr1g0317811' => 'rch', 'RcHm_v2.0_Chr2g0086011' => 'rch', 'RcHm_v2.0_Chr5g0022921' => 'rch', 'RcHm_v2.0_Chr5g0056171' => 'rch', 'Rhsim02G0148600' => 'rsi', 'Rhsim04G0015700' => 'rsi', 'Rhsim06G0225500' => 'rsi', 'Rhsim10G0128300' => 'rsi', 'Rhsim13G0109400' => 'rsi', 'Sabra06G0143400' => 'sbr', 'Sabra16G0238000' => 'sbr', 'Sabra18G0093400' => 'sbr', 'SalBow1G1365' => 'sbo', 'Sc03g0008160' => 'sci', 'Sc08g0004990' => 'sci', 'Sc16g0003510' => 'sci', 'Sc18g0000030' => 'sci', 'Sed0001590' => 'sed', 'Sed0011673' => 'sed', 'Sed0018507' => 'sed', 'SEGI_04254' => 'sgi', 'SEGI_14287' => 'sgi', 'SEGI_28821' => 'sgi', 'SEGI_37253' => 'sgi', 'SEGI_39432' => 'sgi', 'SEGI_39985' => 'sgi', 'SGA_v2.0_scaffold168G38514' => 'sas', 'SGA_v2.0_scaffold265G46129' => 'sas', 'SGA_v2.0_scaffold478G52225' => 'sas', 'SGA_v2.0_scaffold8G04378' => 'sas', 'SHI02628' => 'shi', 'SHI26549' => 'shi', 'SHI26555' => 'shi', 'SMO144G0083' => 'smo', 'Solyc02g014530.4' => 'sly', 'Solyc07g065120.3' => 'sly', 'Solyc12g014570.2' => 'sly', 'Sopen02g003070' => 'spe', 'Sopen02g003890' => 'spe', 'Sopen07g033330' => 'spe', 'Sopen12g007450' => 'spe', 'Sp3g18520' => 'spa', 'Sp5g21930' => 'spa', 'Sp6g17360' => 'spa', 'Sp7g24660' => 'spa', 'SpUn0870_0010' => 'spa', 'TAR383G0611' => 'tar', 'TAR624G0008' => 'tar', 'TAR626G1190' => 'tar', 'TAR626G1861' => 'tar', 'TAR627G0230' => 'tar', 'TAR627G1102' => 'tar', 'THA.LOC104811645' => 'tha', 'THA.LOC104811840' => 'tha', 'THA.LOC104817695' => 'tha', 'THA.LOC104817875' => 'tha', 'Thecc.07G024800' => 'tca', 'Thecc.09G034000' => 'tca', 'Thhalv10012748m.g' => 'esa', 'Thhalv10012762m.g' => 'esa', 'Thhalv10018170m.g' => 'esa', 'Thhalv10020151m.g' => 'esa', 'Thhalv10024494m.g' => 'esa', 'TPR.G14543' => 'tpr', 'TPR.G20448' => 'tpr', 'TPR.G23626' => 'tpr', 'TPR.G30635' => 'tpr', 'TPR.G30657' => 'tpr', 'TPR.G37051' => 'tpr', 'TPR.G5158' => 'tpr', 'TPR.G5159' => 'tpr', 'TWI32G1019' => 'twi', 'TWI34G0602' => 'twi', 'TWI38G0394' => 'twi', 'TWI39G1190' => 'twi', 'unitig_0.g514' => 'ugi', 'unitig_61.g26142' => 'ugi', 'vmacro08428' => 'vma', 'vmacro09678' => 'vma', 'vmacro11328' => 'vma', 'vmacro11569' => 'vma', 'vmacro11572' => 'vma', 'vmacro12764' => 'vma', 'vmacro12765' => 'vma', 'vmacro13031' => 'vma', 'VMungo0540G0685' => 'vmu', 'VMungo0540G2303' => 'vmu', 'VMungo0647G0322' => 'vmu', 'VMungo0647G0427' => 'vmu', 'VMungo0647G1433' => 'vmu', 'VMungo1215G1649' => 'vmu', 'Zm00001eb034650' => 'zma', 'Zm00001eb183390' => 'zma', 'Zm00001eb199730' => 'zma', 'Zm00001eb206420' => 'zma', 'Zm00001eb234640' => 'zma', 'Zm00001eb245640' => 'zma', 'Zm00001eb327550' => 'zma', 'Zm00001eb424720' => 'zma' ) $gf_id = 'HOM05D001160' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001160' ) $data_identifier = 'HOM05D001160' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 36, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 8, 'aox' => (int) 2, 'arhy' => (int) 6, 'ath' => (int) 7, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 28, 'bol' => (int) 18, 'bra' => (int) 19, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 1, 'cil' => (int) 10, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 5, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 8, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 12, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 13, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 8, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 5, 'tpr' => (int) 8, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 8, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424720' $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